MatNormalization: The MatNormalization class
Description
Package: aroma.affymetrix
Class MatNormalization
Object
~~|
~~+--AromaTransform
~~~~~~~|
~~~~~~~+--Transform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--ProbeLevelTransform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--ProbeLevelTransform3
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--AbstractProbeSequenceNormalization
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--MatNormalization
Directly known subclasses:
public static class MatNormalization
extends AbstractProbeSequenceNormalization
This class represents a normalization method that corrects for systematic
effects in the probe intensities due to differences in the number of
A, C, G, and T:s and the match scores according to MAT [1].Usage
MatNormalization(..., unitsToFit=NULL, model=c("lm"), nbrOfBins=200)Arguments
unitsToFit
The units from which the normalization curve should
be estimated. If NULL, all are considered. model
A character string specifying the model used to fit
the base-count effects. nbrOfBins
The number of bins to use for the variance smoothing step.
Fields and Methods
Methods:
rll{
process Normalizes the data set.
}
Methods inherited from AbstractProbeSequenceNormalization:
fitOne, getAromaCellSequenceFile, getTargetFile, indexOfMissingSequences, predictOne, process
Methods inherited from ProbeLevelTransform3:
clearCache, getCellsTo, getCellsToFit, getCellsToUpdate, getUnitsTo, getUnitsToFit, getUnitsToUpdate, writeSignals
Methods inherited from Transform:
getOutputDataSet, getOutputDataSetOLD20090509, getOutputFiles
Methods inherited from AromaTransform:
getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getTags, isDone, process, setTags
Methods inherited from Object:
asThis, getChecksum, $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, saveRequirements
This class requires that an aroma probe sequence file and aroma
match scores file is available for the chip type.References
[1] Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS, Brown M, Liu XS.
Model-based analysis of tiling-arrays for ChIP-chip, PNAS, 2006.